There is an urgent need for a technology to rapidly and cost-effectively analyze genomic DNA for the presence of cancer-related rearrangements, especially those large rearrangements for which no efficient detection method exists. Here we propose the development of a new assay that would make possible very rapid and low cost identification and quantification of rearrangements in genomic DNA without the need for cell culturing, microscope scoring, or sequence amplification. If successfully developed, the assay would detect target sequences located any distance from each other as long as they are both on the same contiguous nucleic acid fragment. The ability to work with large fragments greatly increases the detectability of such rearrangements and hence would provide a powerful tool for cancer diagnostics, research, and screening. Based on our preliminary studies, the assay would require only seconds to "score" the number of chromosomal translocations typically taking weeks or even months of very costly technician time by available cytogenetic methods. The goal of this Phase I proposal is to demonstrate assay feasibility by developing reliable detection of DNA rearrangements in a model system, i.e., large genomic rearrangements in breast cancer (BRCA) genes previously evaluated by Myriad Genetics. Importantly, this work will be performed in close collaboration with Myriad Genetics, the world's foremost experts in breast cancer genetics. The specific aims of this Phase I proposal are: (1) to construct the assay components for detection of large rearrangements in BRCA genes and (2) to use these components/reagents to evaluate assay performance. Acceptable performance is defined as reliable detection of the selected target rearrangement in blind solutions of genomic DNA. PROPOSED COMMERCIAL APPLICATION: It is anticipated that the various embodiments of this technology will result in a number of products and services, including: testing for cancer (and other diseases) by efficiently identifying specific rearrangements; testing for prior radiation or chemical exposures; testing for patient response (and recurrence) to cancer treatments; R&D method (service) for determining correlation of disease with currently unidentified translocations; screening genomic DNA samples for the identification of previously unknown rearrangements that may be linked to cancer; kits for laboratory and research use; add-on instruments specifically for laboratory use (e.g. designed for use with kits); and instrumentation designed for fieldable assay formats.